Genetics Selection Evolution最新文献

{"title":"Genetic analysis of the blood transcriptome of young healthy pigs to improve disease resilience","authors":"Kyu-Sang Lim, Jian Cheng, Christopher Tuggle, Michael Dyck, PigGen Canada, Frederic Fortin, John Harding, Graham Plastow, Jack Dekkers","doi":"10.1186/s12711-023-00860-9","DOIUrl":"https://doi.org/10.1186/s12711-023-00860-9","url":null,"abstract":"Disease resilience is the ability of an animal to maintain productive performance under disease conditions and is an important selection target. In pig breeding programs, disease resilience must be evaluated on selection candidates without exposing them to disease. To identify potential genetic indicators for disease resilience that can be measured on selection candidates, we focused on the blood transcriptome of 1594 young healthy pigs with subsequent records on disease resilience. Transcriptome data were obtained by 3’mRNA sequencing and genotype data were from a 650 K genotyping array. Heritabilities of the expression of 16,545 genes were estimated, of which 5665 genes showed significant estimates of heritability (p < 0.05), ranging from 0.05 to 0.90, with or without accounting for white blood cell composition. Genes with heritable expression levels were spread across chromosomes, but were enriched in the swine leukocyte antigen region (average estimate > 0.2). The correlation of heritability estimates with the corresponding estimates obtained for genes expressed in human blood was weak but a sizable number of genes with heritable expression levels overlapped. Genes with heritable expression levels were significantly enriched for biological processes such as cell activation, immune system process, stress response, and leukocyte activation, and were involved in various disease annotations such as RNA virus infection, including SARS-Cov2, as well as liver disease, and inflammation. To estimate genetic correlations with disease resilience, 3205 genotyped pigs, including the 1594 pigs with transcriptome data, were evaluated for disease resilience following their exposure to a natural polymicrobial disease challenge. Significant genetic correlations (p < 0.05) were observed with all resilience phenotypes, although few exceeded expected false discovery rates. Enrichment analysis of genes ranked by estimates of genetic correlations with resilience phenotypes revealed significance for biological processes such as regulation of cytokines, including interleukins and interferons, and chaperone mediated protein folding. These results suggest that expression levels in the blood of young healthy pigs for genes in biological pathways related to immunity and endoplasmic reticulum stress have potential to be used as genetic indicator traits to select for disease resilience.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138571083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The genetics of gaits in Icelandic horses goes beyond DMRT3, with RELN and STAU2 identified as two new candidate genes","authors":"Heiðrún Sigurðardóttir, Henrik Boije, Elsa Albertsdóttir, Thorvaldur Kristjansson, Marie Rhodin, Gabriella Lindgren, Susanne Eriksson","doi":"10.1186/s12711-023-00863-6","DOIUrl":"https://doi.org/10.1186/s12711-023-00863-6","url":null,"abstract":"In domesticated animals, many important traits are complex and regulated by a large number of genes, genetic interactions, and environmental influences. The ability of Icelandic horses to perform the gait ‘pace’ is largely influenced by a single mutation in the DMRT3 gene, but genetic modifiers likely exist. The aim of this study was to identify novel genetic factors that influence pacing ability and quality of the gait through a genome-wide association study (GWAS) and correlate new findings to previously identified quantitative trait loci (QTL) and mutations. Three hundred and seventy-two Icelandic horses were genotyped with the 670 K+ Axiom Equine Genotyping Array, of which 362 had gait scores from breeding field tests. A GWAS revealed several SNPs on Equus caballus chromosomes (ECA) 4, 9, and 20 that were associated (p < 1.0 × 10–5) with the breeding field test score for pace. The two novel QTL on ECA4 and 9 were located within the RELN and STAU2 genes, respectively, which have previously been associated with locomotor behavior in mice. Haplotypes were identified and the most frequent one for each of these two QTL had a large favorable effect on pace score. The second most frequent haplotype for the RELN gene was positively correlated with scores for tölt, trot, gallop, and canter. Similarly, the second most frequent haplotype for the STAU2 gene had favorable effects on scores for trot and gallop. Different genotype ratios of the haplotypes in the RELN and STAU2 genes were also observed in groups of horses with different levels of pacing ability. Furthermore, interactions (p < 0.05) were detected for the QTL in the RELN and STAU2 genes with the DMRT3 gene. The novel QTL on ECA4, 9, and 20, along with the effects of the DMRT3 variant, were estimated to account jointly for 27.4% of the phenotypic variance of the gait pace. Our findings provide valuable information about the genetic architecture of pace beyond the contribution of the DMRT3 gene and indicate genetic interactions that contribute to the complexity of this trait. Further investigation is needed to fully understand the underlying genetic factors and interactions.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138565079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits","authors":"Klavdija Poklukar, Camille Mestre, Martin Škrlep, Marjeta Čandek-Potokar, Cristina Ovilo, Luca Fontanesi, Juliette Riquet, Samuele Bovo, Giuseppina Schiavo, Anisa Ribani, Maria Muñoz, Maurizio Gallo, Ricardo Bozzi, Rui Charneca, Raquel Quintanilla, Goran Kušec, Marie-José Mercat, Christoph Zimmer, Violeta Razmaite, Jose P. Araujo, Čedomir Radović, Radomir Savić, Danijel Karolyi, Bertrand Servin","doi":"10.1186/s12711-023-00858-3","DOIUrl":"https://doi.org/10.1186/s12711-023-00858-3","url":null,"abstract":"Intense selection of modern pig breeds has resulted in genetic improvement of production traits while the performance of local pig breeds has remained lower. As local pig breeds have been bred in extensive systems, they have adapted to specific environmental conditions, resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds that have been genetically characterized using DNA-pool sequencing data and phenotypically characterized using breed level phenotypes related to stature, fatness, growth, and reproductive performance traits. These data were analyzed using a dedicated approach to detect signatures of selection linked to phenotypic traits in order to uncover potential candidate genes that may underlie adaptation to specific environments. Analysis of the genetic data of European pig breeds revealed four main axes of genetic variation represented by the Iberian and three modern breeds (i.e. Large White, Landrace, and Duroc). In addition, breeds clustered according to their geographical origin, for example French Gascon and Basque breeds, Italian Apulo Calabrese and Casertana breeds, Spanish Iberian, and Portuguese Alentejano breeds. Principal component analysis of the phenotypic data distinguished the larger and leaner breeds with better growth potential and reproductive performance from the smaller and fatter breeds with low growth and reproductive efficiency. Linking the signatures of selection with phenotype identified 16 significant genomic regions associated with stature, 24 with fatness, 2 with growth, and 192 with reproduction. Among them, several regions contained candidate genes with possible biological effects on stature, fatness, growth, and reproductive performance traits. For example, strong associations were found for stature in two regions containing, respectively, the ANXA4 and ANTXR1 genes, for fatness in a region containing the DNMT3A and POMC genes and for reproductive performance in a region containing the HSD17B7 gene. In this study on European local pig breeds, we used a dedicated approach for detecting signatures of selection that were supported by phenotypic data at the breed level to identify potential candidate genes that may have adapted to different living environments and production systems.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138544890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic parameters, reciprocal cross differences, and age-related heterosis of egg-laying performance in chickens","authors":"Aixin Ni, Mario P. L. Calus, Henk Bovenhuis, Jingwei Yuan, Yuanmei Wang, Yanyan Sun, Jilan Chen","doi":"10.1186/s12711-023-00862-7","DOIUrl":"https://doi.org/10.1186/s12711-023-00862-7","url":null,"abstract":"Egg-laying performance is economically important in poultry breeding programs. Crossbreeding between indigenous and elite commercial lines to exploit heterosis has been an upward trend in traditional layer breeding for niche markets. The objective of this study was to analyse the genetic background and to estimate the heterosis of longitudinal egg-laying traits in reciprocal crosses between an indigenous Beijing-You and an elite commercial White Leghorn layer line. Egg weights were measured for the first three eggs, monthly from 28 to 76 weeks of age, and at 86 and 100 weeks of age. Egg quality traits were measured at 32, 54, 72, 86, and 100 weeks of age. Egg production traits were measured from the start of lay until 43, 72, and 100 weeks of age. Heritabilities and phenotypic and genetic correlations were estimated. Heterosis was estimated as the percentage difference of performance of a crossbred from that of the parental average. Reciprocal cross differences were estimated as the difference between the reciprocal crossbreds as a percentage of the parental average. Estimates of heritability of egg weights ranged from 0.29 to 0.75. Estimates of genetic correlations between egg weights at different ages ranged from 0.72 to 1.00. Estimates of heritability for cumulative egg numbers until 43, 72, and 100 weeks of age were around 0.15. Estimates of heterosis for egg weight and cumulative egg number increased with age, ranging from 1.0 to 9.0% and from 1.4 to 11.6%, respectively. From 72 to 100 weeks of age, crossbreds produced more eggs per week than the superior parent White Leghorn (3.5 eggs for White Leghorn, 3.8 and 3.9 eggs for crossbreds). Heterosis for eggshell thickness ranged from 2.7 to 6.6% when using Beijing-You as the sire breed. No significant difference between reciprocal crosses was observed for the investigated traits, except for eggshell strength at 54 weeks of age. The heterosis was substantial for egg weight and cumulative egg number, and increased with age, suggesting that non-additive genetic effects are important in crossbreds between the indigenous and elite breeds. Generally, the crossbreds performed similar to or even outperformed the commercial White Leghorns for egg production persistency.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138544702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of population structure in the estimation of recent historical effective population size by the software GONE","authors":"Irene Novo, Pilar Ordás, Natalia Moraga, Enrique Santiago, Humberto Quesada, Armando Caballero","doi":"10.1186/s12711-023-00859-2","DOIUrl":"https://doi.org/10.1186/s12711-023-00859-2","url":null,"abstract":"Effective population size (Ne) is a crucial parameter in conservation genetics and animal breeding. A recent method, implemented by the software GONE, has been shown to be rather accurate in estimating recent historical changes in Ne from a single sample of individuals. However, GONE estimations assume that the population being studied has remained isolated for a period of time, that is, without migration or confluence of other populations. If this occurs, the estimates of Ne can be heavily biased. In this paper, we evaluate the impact of migration and admixture on the estimates of historical Ne provided by GONE through a series of computer simulations considering several scenarios: (a) the mixture of two or more ancestral populations; (b) subpopulations that continuously exchange individuals through migration; (c) populations receiving migrants from a large source; and (d) populations with balanced systems of chromosomal inversions, which also generate genetic structure. Our results indicate that the estimates of historical Ne provided by GONE may be substantially biased when there has been a recent mixture of populations that were previously separated for a long period of time. Similarly, biases may occur when the rate of continued migration between populations is low, or when chromosomal inversions are present at high frequencies. However, some biases due to population structuring can be eliminated by conducting population structure analyses and restricting the estimation to the differentiated groups. In addition, disregarding the genomic regions that are involved in inversions can also remove biases in the estimates of Ne. Different kinds of deviations from isolation and panmixia of the populations can generate biases in the recent historical estimates of Ne. Therefore, estimation of past demography could benefit from performing population structure analyses beforehand, by mitigating the impact of these biases on historical Ne estimates.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138481040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic correlations of direct and indirect genetic components of social dominance with fitness and morphology traits in cattle","authors":"Beniamino Tuliozi, Roberto Mantovani, Ivana Schoepf, Shogo Tsuruta, Enrico Mancin, Cristina Sartori","doi":"10.1186/s12711-023-00845-8","DOIUrl":"https://doi.org/10.1186/s12711-023-00845-8","url":null,"abstract":"Within the same species, individuals show marked variation in their social dominance. Studies on a handful of populations have indicated heritable genetic variation for this trait, which is determined by both the genetic background of the individual (direct genetic effect) and of its opponent (indirect genetic effect). However, the evolutionary consequences of selection for this trait are largely speculative, as it is not a usual target of selection in livestock populations. Moreover, studying social dominance presents the challenge of working with a phenotype with a mean value that cannot change in the population, as for every winner of an agonistic interaction there will necessarily be a loser. Thus, to investigate what could be the evolutionary response to selection for social dominance, it is necessary to focus on traits that might be correlated with it. This study investigated the genetic correlations of social dominance, both direct and indirect, with several morphology and fitness traits. We used a dataset of agonistic contests involving cattle (Bos taurus): during these contests, pairs of cows compete in ritualized interactions to assess social dominance. The outcomes of 37,996 dominance interactions performed by 8789 cows over 20 years were combined with individual data for fertility, mammary health, milk yield and morphology and analysed using bivariate animal models including indirect genetic effects. We found that winning agonistic interactions has a positive genetic correlation with more developed frontal muscle mass, lower fertility, and poorer udder health. We also discovered that the trends of changes in the estimated breeding values of social dominance, udder health and more developed muscle mass were consistent with selection for social dominance in the population. We present evidence that social dominance is genetically correlated with fitness traits, as well as empirical evidence of the possible evolutionary trade-offs between these traits. We show that it is feasible to estimate genetic correlations involving dyadic social traits.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138455548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Micro-genetic environmental sensitivity across macro-environments of chickens reared in Burkina Faso and France","authors":"Mette Dam Madsen, Naomi Duijvesteijn, Julius van der Werf, Sam Clark","doi":"10.1186/s12711-023-00854-7","DOIUrl":"https://doi.org/10.1186/s12711-023-00854-7","url":null,"abstract":"Commercial poultry production systems follow a pyramidal structure with a nucleus of purebred animals under controlled conditions at the top and crossbred animals under commercial production conditions at the bottom. Genetic correlations between the same phenotypes on nucleus and production animals can therefore be influenced by differences both in purebred-crossbred genotypes and in genotype-by-environment interactions across the two environments, known as macro-genetic environmental sensitivity (GES). Within each environment, genotype-by-environment interactions can also occur due to so-called micro-GES. Micro-GES causes heritable variation in phenotypes and decreases uniformity. In this study, genetic variances of body weight (BW) and of micro-GES of BW and the impacts of purebred-crossbred differences and macro-environmental differences on micro-GES of BW were estimated. The dataset contained three subpopulations of slow-growing broiler chickens: purebred chickens (PB) reared in France, and crossbred chickens reared in France (FR) under the same conditions as PB or reared in Burkina Faso (BF) under local conditions. The crossbred chickens were offspring of the same dam line and had PB as their sire line. Estimates of heritability of BW and micro-GES of BW were 0.54 (SE of 0.02) and 0.06 (0.01), 0.67 (0.03) and 0.03 (0.01), and 0.68 (0.04) and 0.02 (0.01) for the BF, FR, and PB subpopulations, respectively. Estimates of the genetic correlations for BW between the three subpopulations were moderately positive (0.37 to 0.53) and those for micro-GES were weakly to moderately positive (0.01 to 0.44). The results show that the heritability of the micro-GES of BW varies with macro-environment, which indicates that responses to selection are expected to differ between macro-environments. The weak to moderate positive genetic correlations between subpopulations indicate that both macro-environmental differences and purebred-crossbred differences can cause re-ranking of sires based on their estimated breeding values for micro-GES of BW. Thus, the sire that produces the most variable progeny in one macro-environment may not be the one that produces the most variable offspring in another. Similarly, the sire that produces the most variable purebred progeny may not produce the most variable crossbred progeny. The results highlight the need for investigating micro-GES for all subpopulations included in the selection scheme, to ensure optimal genetic gain in all subpopulations.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138455549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sequenced-based GWAS for linear classification traits in Belgian Blue beef cattle reveals new coding variants in genes regulating body size in mammals","authors":"José Luis Gualdrón Duarte, Can Yuan, Ann-Stephan Gori, Gabriel C. M. Moreira, Haruko Takeda, Wouter Coppieters, Carole Charlier, Michel Georges, Tom Druet","doi":"10.1186/s12711-023-00857-4","DOIUrl":"https://doi.org/10.1186/s12711-023-00857-4","url":null,"abstract":"Cohorts of individuals that have been genotyped and phenotyped for genomic selection programs offer the opportunity to better understand genetic variation associated with complex traits. Here, we performed an association study for traits related to body size and muscular development in intensively selected beef cattle. We leveraged multiple trait information to refine and interpret the significant associations. After a multiple-step genotype imputation to the sequence-level for 14,762 Belgian Blue beef (BBB) cows, we performed a genome-wide association study (GWAS) for 11 traits related to muscular development and body size. The 37 identified genome-wide significant quantitative trait loci (QTL) could be condensed in 11 unique QTL regions based on their position. Evidence for pleiotropic effects was found in most of these regions (e.g., correlated association signals, overlap between credible sets (CS) of candidate variants). Thus, we applied a multiple-trait approach to combine information from different traits to refine the CS. In several QTL regions, we identified strong candidate genes known to be related to growth and height in other species such as LCORL-NCAPG or CCND2. For some of these genes, relevant candidate variants were identified in the CS, including three new missense variants in EZH2, PAPPA2 and ADAM12, possibly two additional coding variants in LCORL, and candidate regulatory variants linked to CCND2 and ARMC12. Strikingly, four other QTL regions associated with dimension or muscular development traits were related to five (recessive) deleterious coding variants previously identified. Our study further supports that a set of common genes controls body size across mammalian species. In particular, we added new genes to the list of those associated with height in both humans and cattle. We also identified new strong candidate causal variants in some of these genes, strengthening the evidence of their causality. Several breed-specific recessive deleterious variants were identified in our QTL regions, probably as a result of the extreme selection for muscular development in BBB cattle.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138449744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heterogeneity in convergence behaviour of the single-step SNP-BLUP model across different effects and animal groups","authors":"Dawid Słomian, Kacper Żukowski, Joanna Szyda","doi":"10.1186/s12711-023-00856-5","DOIUrl":"https://doi.org/10.1186/s12711-023-00856-5","url":null,"abstract":"The single-step model is becoming increasingly popular for national genetic evaluations of dairy cattle due to the benefits that it offers such as joint breeding value estimation for genotyped and ungenotyped animals. However, the complexity of the model due to a large number of correlated effects can lead to significant computational challenges, especially in terms of accuracy and efficiency of the preconditioned conjugate gradient method used for the estimation. The aim of this study was to investigate the effect of pedigree depth on the model's overall convergence rate as well as on the convergence of different components of the model, in the context of the single-step single nucleotide polymorphism best linear unbiased prediction (SNP-BLUP) model. The results demonstrate that the dataset with a truncated pedigree converged twice as fast as the full dataset. Still, both datasets showed very high Pearson correlations between predicted breeding values. In addition, by comparing the top 50 bulls between the two datasets we found a high correlation between their rankings. We also analysed the specific convergence patterns underlying different animal groups and model effects, which revealed heterogeneity in convergence behaviour. Effects of SNPs converged the fastest while those of genetic groups converged the slowest, which reflects the difference in information content available in the dataset for those effects. Pre-selection criteria for the SNP set based on minor allele frequency had no impact on either the rate or pattern of their convergence. Among different groups of individuals, genotyped animals with phenotype data converged the fastest, while non-genotyped animals without own records required the largest number of iterations. We conclude that pedigree structure markedly impacts the convergence rate of the optimisation which is more efficient for the truncated than for the full dataset.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138297318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Defining valid breeding goals for animal breeds.","authors":"Robin Wellmann, Nicolas Gengler, Jörn Bennewitz, Jens Tetens","doi":"10.1186/s12711-023-00855-6","DOIUrl":"10.1186/s12711-023-00855-6","url":null,"abstract":"<p><strong>Background: </strong>The objective of any valid breeding program is to increase the suitability of a breed for its future purposes. The approach most often followed in animal breeding for optimizing breeding goals assumes that the sole desire of the owners is profit maximization. As this assumption is often violated, a generalized approach is needed that does not rely on this assumption.</p><p><strong>Results: </strong>The generalized approach is based on the niche concept. The niche of a breed is a set of environments in which a small population of the breed would have a positive population growth rate. Its growth rate depends on demand from prospective consumers and supply from producers. The approach involves defining the niche that is envisaged for the breed and identifying the trait optima that maximize the breed's adaptation to its envisaged niche within the set of permissible breeding goals. The set of permissible breeding goals is the set of all potential breeding goals that are compatible with animal welfare and could be reached within the planning horizon of the breeding program. In general, the breed's adaptation depends on the satisfaction of the producers with the animals and on the satisfaction of the consumers with the products produced by the animals. When consumers buy live animals, then the breed needs to adapt to both the environments provided by the producers, and the environments provided by the consumers. The profit function is replaced by a more general adaptedness function that measures the breed's adaptation to its envisaged niche.</p><p><strong>Conclusions: </strong>The proposed approach coincides with the traditional approach if the producers have the sole desire to maximize their income, and if consumer preferences are well reflected by the product prices. If these assumptions are not met, then the traditional approach to breeding goal optimization is unlikely to result in a valid breeding goal. Using the example of companion breeds, this paper shows that the proposed approach has the potential to fill the gap.</p>","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10664641/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138292467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}